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HaplotypeCaller is now an AnnotatorCompatibleWalker with all the rights and privileges pertaining thereto. Enabling the ClippingRankSumTest after showing it was useful for 1000 Genomes calling.

This commit is contained in:
Ryan Poplin 2012-07-17 14:38:36 -04:00
parent 836f882c30
commit 6efbcd99f1
5 changed files with 8 additions and 5 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@ -15,7 +16,7 @@ import java.util.*;
* The u-based z-approximation from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele).
* Note that the base quality rank sum test can not be calculated for homozygous sites.
*/
public class BaseQualityRankSumTest extends RankSumTest {
public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnotation {
public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine("BaseQRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities")); }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
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@ -18,7 +18,7 @@ import java.util.*;
* Date: 6/28/12
*/
public class ClippingRankSumTest /*extends RankSumTest*/ {
public class ClippingRankSumTest extends RankSumTest {
public List<String> getKeyNames() { return Arrays.asList("ClippingRankSum"); }

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -16,7 +17,7 @@ import java.util.*;
* The u-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele)
* Note that the mapping quality rank sum test can not be calculated for homozygous sites.
*/
public class MappingQualityRankSumTest extends RankSumTest {
public class MappingQualityRankSumTest extends RankSumTest implements StandardAnnotation {
public List<String> getKeyNames() { return Arrays.asList("MQRankSum"); }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
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@ -28,7 +28,7 @@ import java.util.Map;
/**
* Abstract root for all RankSum based annotations
*/
public abstract class RankSumTest extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveRegionBasedAnnotation {
static final double INDEL_LIKELIHOOD_THRESH = 0.1;
static final boolean DEBUG = false;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -4,6 +4,7 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@ -21,7 +22,7 @@ import java.util.*;
* The u-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error).
* Note that the read position rank sum test can not be calculated for homozygous sites.
*/
public class ReadPosRankSumTest extends RankSumTest {
public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotation {
public List<String> getKeyNames() {
return Arrays.asList("ReadPosRankSum");